feat: unit test and refactoring

.github/scripts/nftest_coverage_comment.sh

@@ -0,0 +1,120 @@
+#!/usr/bin/env bash
+
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -euo pipefail
+
+FILE=$1
+if [[ ! -s "$FILE" ]]; then
+  echo "Coverage file $FILE is empty. Exiting."
+  exit 1
+fi
+COVERAGE_THRESHOLD=${COVERAGE_THRESHOLD:-90}
+MARKER="<!-- nf-test-coverage-report -->"
+
+: "${GITHUB_TOKEN:?Missing GITHUB_TOKEN}"
+: "${GITHUB_REPOSITORY:?Missing GITHUB_REPOSITORY}"
+: "${GITHUB_EVENT_PATH:?Missing GITHUB_EVENT_PATH}"
+
+# Get PR number
+PR_NUMBER=$(jq -r '.pull_request.number' "$GITHUB_EVENT_PATH")
+
+if [[ -z "$PR_NUMBER" || "$PR_NUMBER" == "null" ]]; then
+  echo "Not running on a pull request. Exiting."
+  exit 0
+fi
+
+# ---- Parse nf-test coverage totals ----
+COVERAGE_LINE=$(grep -E '(COVERAGE:|Status:)' "$FILE" | tail -1 || true)
+if [[ -z "$COVERAGE_LINE" ]]; then
+  echo "ERROR: Could not find coverage line in $FILE"
+  cat "$FILE"
+  exit 1
+fi
+
+if echo "$COVERAGE_LINE" | grep -q 'COVERAGE:'; then
+  TOTAL_COVERAGE=$(echo "$COVERAGE_LINE" | grep -oE '[0-9]+(\.[0-9]+)?%' | tr -d '%' || true)
+  HIT_FILES=$(echo "$COVERAGE_LINE" | grep -oE '[0-9]+ of' | grep -oE '[0-9]+' || true)
+  TOTAL_FILES=$(echo "$COVERAGE_LINE" | grep -oE 'of [0-9]+' | grep -oE '[0-9]+' || true)
+else
+  # New format: "Status: 26 of 64 modules and workflows are covered ... (40.62%)"
+  TOTAL_COVERAGE=$(echo "$COVERAGE_LINE" | grep -oE '\([0-9]+(\.[0-9]+)?%\)' | tr -d '()%' || true)
+  HIT_FILES=$(echo "$COVERAGE_LINE" | grep -oE '[0-9]+ of' | grep -oE '[0-9]+' || true)
+  TOTAL_FILES=$(echo "$COVERAGE_LINE" | grep -oE 'of [0-9]+' | grep -oE '[0-9]+' || true)
+fi
+
+if [[ -z "$TOTAL_COVERAGE" || \
+    -z "$HIT_FILES" || \
+    -z "$TOTAL_FILES" || "$TOTAL_FILES" -eq 0 ]];
+then
+  echo "Could not parse coverage percentage from: $COVERAGE_LINE"
+  exit 1
+fi
+
+COVERAGE_OK=$(awk -v cov="$TOTAL_COVERAGE" -v th="$COVERAGE_THRESHOLD" \
+  'BEGIN { print (cov >= th) ? "yes" : "no" }')
+
+if [[ "$COVERAGE_OK" == "yes" ]]; then
+  STATUS_ICON="✅"
+  STATUS_TEXT="Coverage meets threshold"
+else
+  STATUS_ICON="❌"
+  STATUS_TEXT="Coverage below ${COVERAGE_THRESHOLD}% threshold"
+fi
+
+
+# ---- Comment body ----
+COMMENT_BODY=$(cat <<EOF
+$MARKER
+### 🧪 nf-test Coverage Report
+
+**Total coverage:** **${TOTAL_COVERAGE}%**  
+**Lines:** $HIT_FILES / $TOTAL_FILES  
+**Status:** $STATUS_ICON $STATUS_TEXT
+EOF
+)
+
+# ---- GitHub API ----
+API_URL="https://api.github.com"
+COMMENTS_URL="$API_URL/repos/$GITHUB_REPOSITORY/issues/$PR_NUMBER/comments"
+AUTH_HEADER="Authorization: Bearer $GITHUB_TOKEN"
+
+EXISTING_COMMENT_ID=$(curl -s \
+  -H "$AUTH_HEADER" \
+  -H "Accept: application/vnd.github+json" \
+  "$COMMENTS_URL" \
+  | jq -r ".[] | select(.body | contains(\"$MARKER\")) | .id")
+
+if [[ -n "$EXISTING_COMMENT_ID" ]]; then
+  echo "Updating existing nf-test coverage comment"
+  curl -s -X PATCH \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$API_URL/repos/$GITHUB_REPOSITORY/issues/comments/$EXISTING_COMMENT_ID" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+else
+  echo "Creating nf-test coverage comment"
+  curl -s -X POST \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$COMMENTS_URL" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+fi
+
+# ---- Fail CI if coverage too low ----
+if [[ "$COVERAGE_OK" != "yes" ]]; then
+  echo "Coverage ${TOTAL_COVERAGE}% is below threshold ${COVERAGE_THRESHOLD}%"
+  exit 1
+fi

.github/scripts/py_coverage_comment.sh

@@ -0,0 +1,127 @@
+#!/usr/bin/env bash
+
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -euo pipefail
+
+LCOV_FILE=$1
+if [[ ! -s "$LCOV_FILE" ]]; then
+  echo "Coverage file $LCOV_FILE is empty. Exiting."
+  exit 1
+fi
+COVERAGE_THRESHOLD=${COVERAGE_THRESHOLD:-90}
+MARKER="<!-- python-lcov-coverage-report -->"
+
+: "${GITHUB_TOKEN:?Missing GITHUB_TOKEN}"
+: "${GITHUB_REPOSITORY:?Missing GITHUB_REPOSITORY}"
+: "${GITHUB_EVENT_PATH:?Missing GITHUB_EVENT_PATH}"
+
+# Get PR number
+PR_NUMBER=$(jq -r '.pull_request.number' "$GITHUB_EVENT_PATH")
+
+if [[ -z "$PR_NUMBER" || "$PR_NUMBER" == "null" ]]; then
+  echo "Not running on a pull request. Exiting."
+  exit 0
+fi
+
+# ---- Parse LCOV totals ----
+TOTAL_LINES=$(grep -h '^LF:' "$LCOV_FILE" | awk -F: '{sum += $2} END {print sum}')
+HIT_LINES=$(grep -h '^LH:' "$LCOV_FILE" | awk -F: '{sum += $2} END {print sum}')
+
+if [[ -z "$TOTAL_LINES" || "$TOTAL_LINES" -eq 0 ]]; then
+  echo "Failed to parse LCOV file"
+  exit 1
+fi
+
+TOTAL_COVERAGE=$(awk -v hit="$HIT_LINES" -v total="$TOTAL_LINES" \
+  'BEGIN { printf "%.2f", (hit / total) * 100 }')
+
+COVERAGE_OK=$(awk -v cov="$TOTAL_COVERAGE" -v th="$COVERAGE_THRESHOLD" \
+  'BEGIN { print (cov >= th) ? "yes" : "no" }')
+
+if [[ "$COVERAGE_OK" == "yes" ]]; then
+  STATUS_ICON="✅"
+  STATUS_TEXT="Coverage meets threshold"
+else
+  STATUS_ICON="❌"
+  STATUS_TEXT="Coverage below ${COVERAGE_THRESHOLD}% threshold"
+fi
+
+# ---- Per-file coverage table ----
+TABLE=$(awk '
+BEGIN {
+  print "| File | Coverage |"
+  print "|------|----------|"
+}
+$1 ~ /^SF:/ { file = substr($1,4); lf=0; lh=0 }
+$1 ~ /^LF:/ { lf = substr($1,4) }
+$1 ~ /^LH:/ { lh = substr($1,4) }
+$1 ~ /^end_of_record/ {
+  if (lf > 0) {
+    printf "| %s | %.2f%% |\n", file, (lh / lf) * 100
+  }
+}
+' "$LCOV_FILE")
+
+# ---- Comment body ----
+COMMENT_BODY=$(cat <<EOF
+$MARKER
+### 🐍 Python Coverage Report (coverage.py / lcov)
+
+**Total coverage:** **${TOTAL_COVERAGE}%**  
+**Lines:** $HIT_LINES / $TOTAL_LINES  
+**Status:** $STATUS_ICON $STATUS_TEXT
+
+<details>
+<summary>Per-file coverage</summary>
+
+$TABLE
+
+</details>
+EOF
+)
+
+# ---- GitHub API ----
+API_URL="https://api.github.com"
+COMMENTS_URL="$API_URL/repos/$GITHUB_REPOSITORY/issues/$PR_NUMBER/comments"
+AUTH_HEADER="Authorization: Bearer $GITHUB_TOKEN"
+
+EXISTING_COMMENT_ID=$(curl -s \
+  -H "$AUTH_HEADER" \
+  -H "Accept: application/vnd.github+json" \
+  "$COMMENTS_URL" \
+  | jq -r ".[] | select(.body | contains(\"$MARKER\")) | .id")
+
+if [[ -n "$EXISTING_COMMENT_ID" ]]; then
+  echo "Updating existing Python coverage comment"
+  curl -s -X PATCH \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$API_URL/repos/$GITHUB_REPOSITORY/issues/comments/$EXISTING_COMMENT_ID" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+else
+  echo "Creating Python coverage comment"
+  curl -s -X POST \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$COMMENTS_URL" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+fi
+
+# ---- Fail CI if coverage too low ----
+if [[ "$COVERAGE_OK" != "yes" ]]; then
+  echo "Coverage ${TOTAL_COVERAGE}% is below threshold ${COVERAGE_THRESHOLD}%"
+  exit 1
+fi

.github/workflows/build.yml

@@ -0,0 +1,45 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: build
+on: workflow_dispatch
+
+env:
+  PYTHON_SRC_DIR: src/python/ensembl
+  RUST_SRC_DIR: src/rust/ensembl
+  BIN_DIR: nextflow/vcf_prepper/bin
+
+jobs:
+  python:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install/Update Dependencies
+        run: python3 -m pip install --upgrade build
+      - name: Build
+        run: python3 -m build ${{ env.PYTHON_SRC_DIR }}
+
+  rust:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        BUILD_TARGET: [
+          bed_to_wig,
+          merge_bed
+          vcf_to_bed
+        ]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build ${{ matrix.BUILD_TARGET }}
+        run: cargo build --manifest_file ${{ env.RUST_SRC_DIR }}/${{ matrix.BUILD_TARGET }}/Cargo.toml --artifact-dir ${{ BIN_DIR }}

.github/workflows/linting.yml

@@ -0,0 +1,47 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: linting
+on: workflow_dispatch
+
+# Make sure CI fails on all warnings, including Clippy lints
+env:
+  RUSTFLAGS: "-Dwarnings"
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Run Ruff Check
+        run: ruff check --output-format=github .
+      - name: Run Ruff Format
+        run: ruff format
+
+  clippy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run Clippy
+        run: cargo clippy --all-targets --all-features
+      - name: Run Rustfmt
+        run: cargo +nightly fmt